Southern California Genotyping Consortium

Table of Contents

Human DNA samples submitted to the SCGC for GoldenGate genotyping should be prepared according to the following guidelines:

Each reaction (1 reaction per oligo pool per sample) requires 1 Ug of genomic DNA (250 ng for the reaction plus dead volume and quant check volume) .
Liquid DNA samples should be normalized in water or 1 X TE to a standard concentration between 100 ng and 200 ng per ul. Samples with concentrations below 50 ng per ul will not be accepted for genotyping and will be returned to you to be concentrated or re-aliquoted. Please err on the high side if possible. The upper limit is fairly flexible, we ask only that samples be completely resuspended and not at all viscous. Please note that we have found Nanodrop spec concentrations to be somewhat variable. If using a nanodrop or other method that requires pipetting very small volumes ( 1-2 ul) please consider that you may be significantly overestimating the true concentration.
As noted above, in addition to the amount of DNA consumed in the reaction itself (assumed to be 5ul even though the sample may have to be diluted prior to genotyping), all samples must be delivered with an extra 5 ul of DNA per sample to confirm the DNA concentration using a PicoGreen assay plus 10 ul of DNA per sample as dead pipetting volume. Any and all DNA left over at the end of a project can be returned to you if you choose but these extra volumes are not optional.
- As an example: A single OPA project (96 to 1536 snps) with DNA normalized to 100 ng/ul would require 5ul for the Pico green quant check and 10 ul as pipetting dead volume and 5ul for the reaction itself for 20 ul total volume.

If contemplating using Whole Genome Amplification products as samples, please inquire.

We require DNA that samples be sent in 96 well format PCR type plates of this specific type:

96 well skirted v-bottom polypropylene microplates Cat# MSP-9601 from Biorad sealed with foil adhesive seals or heat sealed. We’re happy to ship these plates and seals to you if you are unable to obtain the correct plates.
Samples sent in plates other than those listed above will be re-plated into the correct plates and will incur a charge of $100 per plate.

Human Genomic DNA samples submitted to the SCGC for Infinium Whole Genome Genotyping should be prepared according to the following guidelines:

Each reaction (1 sample=1 reaction) requires 4ug of genomic DNA.
Liquid DNA samples should be normalized in 1 X TE to a standard concentration between 100 ng and 200 ng per ul, Samples with concentrations below 50 ng per ul will not be accepted for genotyping and will be returned to you to be concentrated or re-aliquoted. Please err on the high side if possible. The upper limit is fairly flexible, we ask only that samples be completely resuspended and not at all viscous.

Please note that we have found Nanodrop spec concentrations to be somewhat variable. If using a nanodrop or other method that requires pipetting very small volumes (1-2 ul) please consider that you may be significantly overestimating the true concentration.

In addition to the amount of DNA consumed in the reaction itself (750 ng), we also require an extra 5 ul of DNA per sample to confirm the DNA concentration using a PicoGreen assay plus 10-20 ul of DNA per sample as dead pipetting volume. Any and all DNA left over at the end of a project can be returned to you if you choose.

Whole Genome Amplification is not compatible with Infinium Whole Genome Genotyping at this time.

RNA samples submitted to the SCGC for Gene Expression analysis on the Human or Mouse RefSeq 24K genechips should be prepared according to the following guidelines:

Input RNA quality is the most significant factor in overall data quality. Therefore it is highly recommended that all total RNA samples be free of all contaminants (Trizol etc) and be assessed for quality using an Agilent Bioanalyzer.
We require 100 ng total RNA in a volume less than 10 ul for each sample plus 5ul additional RNA for a RiboGreen quant check. We confirm the concentration of all samples using a ribogreen assay. Other methods can give results that are quite different than those generated by ribogreen. For the purposes of this assay, we recommend that you assume that your (non-ribogreen) results are high by a factor of 2.5 and adjust the amount you send to us accordingly. Nothing personal, it just saves time.

General notes:

Individual tubes can also be used for DNA samples for genotyping, however, please note: you must send us an excel spreadsheet listing all sample names and an accurate volume prior to sending us the samples. We’ll then send you a set of sterile, pre-labeled screw cap tubes in a hinged box. Aliquots/ dilutions can then be made directly into these tubes and submitted for genotyping. Genotyping samples sent in tubes other that those provided by the SCGC will be returned to the sender. Gene expression samples are welcome in any kind of tubes at all.

Please note that all submissions must be accompanied by an electronic sample sheet (excel spreadsheet) and a signed letter on official letterhead stating that you have IRB approval to use the samples in question. If you wish for the SCGC to perform Mendel checks on the genotyping results please also provide a family file in linkage format.

Please provide an excel spreadsheet (by email) listing the sample names, volumes and concentrations. Also, please indicate which samples, if any, are Whole Genome Amplified (WGA).

Please notify me by email when samples have been shipped and include the tracking number (and shipper) so I can keep an eye on their progress

My email address is: jdeyoung@mednet.ucla.edu

My phone number is : 1-310-825-2390

The shipping address is:

UCLA Gonda building 695 Charles Young Dr. South Los Angeles, California 90095 Attn: Joe DeYoung Room 3554